Cell-state-specific cis-regulatory logic of pattern-triggered immunity with csRNA-seq and snMultiome

*This is a poster presented at Plant Biology 2026, Ottawa, Canada.

Plant immune responses are tightly regulated, generating transcriptional programs that differ by cell type and state, yet the cis-regulatory elements and transcription factor (TF) networks underlying these cell-state-specific responses remain poorly defined. To address this, we paired two complementary genome-wide assays across a matched flg22 (a flagellin-derived elicitor of pattern-triggered immunity, PTI) time-series in Arabidopsis seedlings. Capped small RNA sequencing (csRNA-seq) mapped active enhancers genome-wide, identifying thousands induced by flg22. Single-nucleus multiome profiling (joint snRNA-seq and snATAC-seq) of the same response resolved tens of thousands of nuclei spanning ten cell types. Comparing the 30-minute and 3-hour samples captured successive waves of activation, with distinct early and later transcriptional programs apparent across both assays. Integrating the two datasets indicates that immune activation is partitioned across the cellular landscape, with cell type-specific enhancer activation. Linking enhancers to their target genes further points to combinatorial TF logic that varies by cell type. Together these observations begin to assemble a cell-state-resolved framework for the cis-regulatory code of plant immunity.